| calculate_all_Area | Calculate Area/Intensity for the whole input sequence dataframe |
| calculate_all_PSM | Calculate Spectra Count (PSM) for the whole input sequence dataframe |
| calculate_Area | Calculate Area/Intensity for one row of the input sequence dataframe |
| calculate_PSM | Calculate Spectra Count (PSM) for one row of the input sequence dataframe |
| combine_files_from_folder | Combine CSV and TXT Files from a Folder |
| convert_to_regex_pattern | Convert Peptide Sequence to Regex Pattern |
| create_peptide_plot | Create a peptide Plot |
| match_and_calculate_positions | Match peptide sequence with provided sequence and calculate positions |
| obtain_mod | Obtain post translational modification(PTM) information from Peptide data based on the specified data type |
| obtain_mod_Comet | Obtain modification information from Peptide data generated by Comet |
| obtain_mod_DIANN | Obtain modification information from Peptide data generated by DIA-NN |
| obtain_mod_Maxquant | Obtain modification information from Peptide data generated by Maxquant |
| obtain_mod_MSFragger | Obtain modification information from Peptide data generated by MSFragger |
| obtain_mod_mzIdenML | Obtain modification information from Peptide data generated by mzIdenML |
| obtain_mod_mzTab | Obtain modification information from Peptide data generated by mzTab |
| obtain_mod_PEAKS | Obtain modification information from Peptide data generated by PEAKS |
| obtain_mod_Skyline | Obtain modification information from Peptide data generated by Skyline |
| obtain_mod_Spectronaut | Obtain modification information from Peptide data generated by Spectronaut |
| peptide_quantification | Peptide Quantification |
| run_pepmap_app | Launch PepMapViz Shiny Application |
| strip_sequence | Strip peptide sequences based on the specified data type |
| strip_sequence_Comet | Strip sequence from Comet outputs |
| strip_sequence_DIANN | Strip sequence from DIANN outputs |
| strip_sequence_Maxquant | Strip sequence from Maxquant outputs |
| strip_sequence_MSFragger | Strip sequence from MSFragger outputs |
| strip_sequence_PEAKS | Strip sequence from PEAKS outputs |
| strip_sequence_Skyline | Strip sequence from Skyline outputs |
| strip_sequence_Spectronaut | Strip sequence from Spectronaut outputs |